[gmx-users] help with poor performance on gromacs on Cray linux

Justin Lemkul jalemkul at vt.edu
Fri Jun 27 02:06:40 CEST 2014

On 6/26/14, 4:54 PM, Tom wrote:
> Justin,
> I compared the peromance (the time spent for mdrun) using md.log files for
> the same simulatin run on Cary Linux and any other Linux system.
> I agree different hardware can have different performance.
> But these tests were run on the supper computer clusters with very good
> reputations of performance. The one on Cray is very slow.

Comparing apples and oranges is very hard.  The .log files should provide lots 
of detail about how mdrun spent its time.  That's what I (and likely others) was 
hoping to see.  It should reveal if there was something really bizarre about the 
run, or if it's something more fundamental.

> I am the first time to run gmc on Cray linux. I am doubting if there is any
> wrong for my installation.

Your sysadmins are going to be a better resource than this community, since we 
know nothing about the specs of the supercomputer.  Even if no one has run 
Gromacs, the sysadmins should know a lot of about getting the most bang for your 
buck in terms of using any system-specific optimizations.

>  From the previous dissusion, gmx looks to have performance problem
> on Cray linux:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-May/081473.html
> I am also wondering if the newest version solved this issue.

The only known issues on Cray have been fixed AFAIK (see, e.g. 



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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